Github install
GitBash install
RStudio install
#created MICB425_portfolio directory on my computer
#created new repository 'MICB_portfolio' on my Github account
git init
git add .
git commit -m "comment text" #comment was 'First commit'
git remode add origin [repository url] #URL was taken from repository page on Github
git remote -v #just to check that URL was correct
git push -u origin master
The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.
http://phdcomics.com/ Comic posted 1-17-2018
The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)
hint: go to the PhD Comics website to see if you can find the image above
If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown
Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).
Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:
1231521+12341556280987
## [1] 1.234156e+13
Or maybe, after you’ve added those numbers, you feel like it’s about time for a table! I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the future.
library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")
| speed | dist | |
|---|---|---|
| Min. : 4.0 | Min. : 2.00 | |
| 1st Qu.:12.0 | 1st Qu.: 26.00 | |
| Median :15.0 | Median : 36.00 | |
| Mean :15.4 | Mean : 42.98 | |
| 3rd Qu.:19.0 | 3rd Qu.: 56.00 | |
| Max. :25.0 | Max. :120.00 |
And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!
The template for the first Evidence Worksheet has been included here. The first thing for any assignment should link(s) to any relevant literature (which should be included as full citations in a module references section below).
You can copy-paste in the answers you recorded when working through the evidence worksheet into this portfolio template.
As you include Evidence worksheets and Problem sets in the future, ensure that you delineate Questions/Learning Objectives/etc. by using headers that are 4th level and greater. This will still create header markings when you render (knit) the document, but will exclude these levels from the Table of Contents. That’s a good thing. You don’t’ want to clutter the Table of Contents too much.
Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.
What effect does the global microbial population have on biogeochemistry?
Available numbers were taken from studies from each small environment. They were converted to the same format and units, then averaged for each environment. Each averaged measurement of an environment was extrapolated to be proportionate to the size of said environment. Then they had to do a fair amount of guesstimation, combined with comparisons to older values to see if their results were within a reasonable order of magnitude. They also calculated the results of sections by different methods to see if all gave the same order of magnitude.
Nearl all prokaryotic life comes from three main environments: aquatic environments, the subsurface, and soil. About half of the global organic C is contained in microbial cells and 90% of global nutrients. This is 10x the nutrients contained in plants globally. They also determined the turnover rate of cells in each environment.
Is the biogeochemical effect in the subsurface large, even if the turnover rate, and therefore microbial activity, is so slow?
I think there were a lot of necessary assumptions made to reach their conclusions, but the reason for each assumption was made clear so I was able to follow the logic of how they reached their conclusions pretty well.
Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.
What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.
Subsurface - Major habitat for prokaryotes, with most of the subsurface biomass supported by organic matter deposited from the surface. Total abundance: 3.8 x 10^30
What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?
What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?
Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?
Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)
Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?
What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?
Utilize this space to include a bibliography of any literature you want associated with this module. We recommend keeping this as the final header under each module.
An example for Whitman and Wiebe (1998) has been included below.
Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863